TB-Profiler

TB-Profiler result

Run: ERR2514443

This average coverage of the target regions is below the recommended 30x. Some mutations may not be detected due to low coverage.

Summary

Run ID: ERR2514443

Sample name:

Date: 2024-04-15T18:35:44.588886

Number of reads: 533274

Percentage reads mapped: 99.53

Median coverage: 16.0

Strain: lineage4.4

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs

Lineage	Family	RDs	Frequency
lineage4	Euro-American	None	1.0
lineage4.4	Euro-American	None	0.97

Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes

Drug	Resistance	Supporting mutations	WHO confidence	Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid

Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance

Gene	Chromosome position	Mutation	Type	Estimated fraction	Drugs	Confidence	Comment

Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance

Gene	Chromosome position	Mutation	Type	Estimated fraction	Drugs	Confidence
gyrB	5509	c.270C>T	synonymous_variant	1.0	levofloxacin	Not assoc w R - Interim
gyrB	5509	c.270C>T	synonymous_variant	1.0	moxifloxacin	Not assoc w R - Interim
gyrB	5915	p.Val226Ile	missense_variant	0.96	levofloxacin
gyrB	5915	p.Val226Ile	missense_variant	0.96	moxifloxacin
gyrA	7362	p.Glu21Gln	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	7362	p.Glu21Gln	missense_variant	1.0	moxifloxacin	Not assoc w R
gyrA	7585	p.Ser95Thr	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	7585	p.Ser95Thr	missense_variant	1.0	moxifloxacin	Not assoc w R
gyrA	9304	p.Gly668Asp	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	9304	p.Gly668Asp	missense_variant	1.0	moxifloxacin	Not assoc w R
Rv0010c	13806	c.-248C>A	upstream_gene_variant	1.0	isoniazid
nusG	734184	c.-70T>C	upstream_gene_variant	1.0	rifampicin	Uncertain significance
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
Rv1258c	1407228	p.Glu38Ala	missense_variant	1.0	streptomycin
					isoniazid
					pyrazinamide
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	streptomycin
					kanamycin
					capreomycin
					amikacin
tsnR	1854300	p.Leu232Pro	missense_variant	1.0	linezolid	Not assoc w R
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Not assoc w R
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Not assoc w R - Interim
Rv2752c	3066099	p.Met31Ile	missense_variant	1.0	ethambutol	Not assoc w R
					moxifloxacin	Uncertain significance
					levofloxacin	Uncertain significance
					rifampicin	Not assoc w R
					isoniazid	Not assoc w R - Interim
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
embC	4238963	c.-900C>T	upstream_gene_variant	1.0	ethambutol	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
embA	4246508	c.3276G>A	synonymous_variant	1.0	ethambutol	Not assoc w R
ubiA	4268928	c.906C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
ubiA	4269375	c.459G>A	synonymous_variant	1.0	ethambutol	Not assoc w R
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	capreomycin	Not assoc w R
					amikacin	Not assoc w R
					kanamycin	Not assoc w R
whiB6	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin